PRIMAL

Pipeline of Root Image analysis
using MAchine Learning.

About PRIMAL

PRIMAL stands for a Pipeline of Root Image analysis using MAchine Learning. In short, the pipeline use Machine Learning techniques (Random Forest in particular), tu streamline the image analysis of large root dataset.

PRIMAL needs only a subset of the data to be analyse manual, instead of the full dataset. That subset is then used to train the algorithm behind PRIMAL the predict the parameters of interest, based on automatically acquired descriptors.

How to use PRIMAL

PRIMAL is an app developped in R, using the Shiny framework. The only requirement is to have a working version of R installed. Then, your R console, type the following lines:

library(shiny)
shiny::runGitHub("plantmodelling/primal", "plantmodelling")

A full description of the PRIMAL protocole can be found on Protocols.io:

PRIMAL protocole . PRIMAL source code

Cite PRIMAL

Combining semi-automated root image analysis techniques with machine learning algorithms to accelerate large scale genetic root studies.
Jonathan A. Atkinson, Guillaume Lobet, Manuel Noll, Markus Griffiths, Darren M. Wells
biorXiv, 2017

Contact the PRIMAL team

PRIMAL was developped as a collaboration between the Forchungszentrum Juelich, The Université de Liège, the Université catholique de Louvain and the University of Nottingham.